Sequence
atgc intronic sequence ATGC exonic sequence...cttccccttccctatttccaggtctttaaggcttcctatgtaactaaaaaaaaaaaagcgattagattgcctttttgtcttatcttttggtgtattacagGTATCAGAAGTGAGTTCACTTTTGGGCCGAGCTGGTACAGCTGGGCTTGGCAAGGCAGTAGAAGTTTTGGACACACTAGGCAGTAGTATGACAAATTTGA
Basic information
species | Glycine max |
transcript | GLYMA20G31400.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G077621_T01 (Zea mays), 3'ss of exon 1
cttccccttccctatttccaggtct---ttaaggcttcctatgtaactaaaaaaaaaa---aagcgattagattgccttt-ttgtcttatcttttggtgtattacagGTATCAGAAGTGAGTTCACTTTTGGGCCGAGCTGGTACAGCTGGGCTTGGCAAGGCAGTAGAAGTTTTGGACACACTAGGCAGTAGTATGACAAATTTGA
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-------tagtatacctcaaagtttaggttagtgcttggtttatggcagagattattagttaggcatctctatcattcatattggttcatttcctgtattcaaacagGTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGTTGGGCTTGAAAAGGCAGTGGAGGTTCTGGACACACTTGGCAGTAGCATGACAAGTTTTA
upper sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G046846_T01 (Zea mays), 3'ss of exon 2
cttccccttccctatttccaggtctttaaggcttcctatgtaactaaaaaaaaaaaagcgattagattgcctttt-tgtcttatcttttggtgtattacagGTATCAGAAGTGAGTTCACTTTTGGGCCGAGCTGGTACAGCTGGGCTTGGCAAGGCAGTAGAAGTTTTGGACACACTAGGCAGTAGTATGACAAATTTGA
| | || | | || || ||| | | | | | || || ||| ||| ||| | | || | | |||| || ||||| || ||| || |||| ||||| |||| ||||| ||||| || ||||| ||||| | |||||||| |||||||| |||||||||||||
ccttaactatttgtccatgaaatgttcaaaaattctgctcggtcagagagattgctagaccctatgccatgtttgatgttctatttccttgt-tgaaatagGTTTCGGAAGTAAGCTCAATTCTGGGTAGAGCTAGTACTGCTGGCCTTGGAAAAGCAGTGGAAGTGCTTGACACACTTGGCAGTAGCATGACAAATTTGA
upper sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G097502_T02 (Zea mays), 3'ss of exon 1
cttccccttccctatttccaggtctttaaggcttcctatgtaactaaaaaa---aaaaaagcgattagattgccttt-ttgtcttatcttttggtgtattacagGTATCAGAAGTGAGTTCACTTTTGGGCCGAGCTGGTACAGCTGGGCTTGGCAAGGCAGTAGAAGTTTTGGACACACTAGGCAGTAGTATGACAAATTTGA
| | | | | |||| ||| ||| | | | | | | | | || | || | ||| | | | || | |||||| ||||||||||| ||| |||| || ||||| | || |||||||||| |||||||| || ||| | || ||||| |||||||| ||||||| ||| |
-tagtacacctcatagtgtaggt---taatgctgtgtttatggcggagattgttaggtaggcatctctatcattcatattggttcctttcctgtattgaaacagGTTTCAGAAGTGAGCTCAATTTTAGGTAGAGCTAGCACTGCTGGGCTTGAAAAGGCAGTGGAGGTTCTAGATACACTTGGCAGTAGCATGACAAGTTTAA
upper sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 1
-cttccccttccctatttccaggtctttaaggc--ttcctatgtaactaaaaaaaaaaaagcgattagattgcctttttgtcttatcttttggtgtattacagGTATCAGAAGTGAGTTCACTTTTGGGCCGAGCTGGTACAGCTGGGCTTGGCAAGGCAGTAGAAGTTTTGGACACACTAGGCAGTAGTATGACAAATTTGA
| | ||| | | ||| | | | | || || | || |||| | || ||| | | |||||| || ||||| ||||||||||| |||||||||||| | |||||||| ||||||||||| |||||||| ||||||||||||||||| || ||||| ||||||||||||
acagaatgatattcattattatattggtaatgtgatgttgaattgtcttaatggatcaatatttttag-tagcactttaatggattgatttggtatac--cagGTTTCAGAAGTGAGCTCACTTTTGGGCAGGGCTGGTACTGCTGGGCTTGGGAAGGCAGTTGAAGTTTTGGACACACTTGGTAGTAGCATGACAAATTTGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaaaaaaaaaagcgattagattgcctttttgtcttatcttttggtgtattacagGTATCAGAAGTGAGTTCACTTTTGGGCCGAGCTGGTACAGCTGGGCTTGGCAAGGCAGTAGAAGTTTTGGACACACTAGGCAGTAGTATGACAAATTTGA
aactaaa putative branch site (score: 2)
ttatctttt TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttccccttccctatttccaggtctttaaggcttcctatgtaactaaaaaaaaaaaagcgattagattgcctttttgtcttatcttttggtgtattacagGTATCAGAAGTGAGTTCACTTTTGGGCCGAGCTGGTACAGCTGGGCTTGGCAAGGCAGTAGAAGTTTTGGACACACTAGGCAGTAGTATGACAAATTTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
cttcccc
- - - - - - - - -ccaggtc
- - - - - - - - - - - - - - - gcttcct
- - - - - - - - - - - - - - - - - - - - - - -aaaaaaa